ENCODE Software
All software used or developed by the ENCODE Consortium
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- dnase-call-hotspots — sourceCalls hotspots and peaks on filtered alignments by hotspot2 for DNase ENCODE uniform processing pipeline.Software type: peak caller
- rampage-peaks — sourcePeak calling by GRIT for Rampage ENCODE uniform processing pipeline.Software type: peak caller
- overlap_peaks.py — sourceoverlap_peaks.py is a method to select overlapping peaks among replicates and psuedo-replicatesSoftware type: peak caller
- F-seq — sourceF-seq is a software package that generates a continuous density estimation of sequence tags mapped to a reference genome, which can be displayed using the UCSC Genome Browser. The continuous density plots are more intuitive than discrete histogram-like plots used by some applications. Using kernel density estimation, F-seq can aid the identification of biologically meaningful sites.Software type: peak caller
- Hotspot — sourceIdentifies regions of local enrichment, including peaks, in genomic short-read sequence data. Uses the binomial distribution with a local background model to automatically correct for broad-scale regional differences in tag levels. It is applicable to a wide variety of epigenetic profiling assays, including ChIP-seq and DNase-seq. Hotspot forms the basis of the SPOT data quality metric.Software type: peak caller
- MACS — sourceA widely-used, fast, robust ChIP-seq peak-finding algorithm that accounts for the offset in forward-strand and reverse-strand reads to improve resolution and uses a dynamic Poisson distribution to effectively capture local biases in the genome. MACS 1.4 was used in the ENCODE 2 uniform peak calling pipeline.Software type: peak caller
- GEM — sourceGEM is a Java software package for analyzing genome wide ChIP-seq/ChIP-exo data. GEM can decompose single observed peaks into multiple binding events, determine binding event location at high spatial resolution, and discover explanatory DNA sequence motifs with an integrated model of ChIP reads and proximal DNA sequences. GEM is able to process single-end or paired-end data and can be run in single-condition mode or multi-condition mode. GEM will be used in the ENCODE 3 uniform peak calling pipeline.Software type: peak caller
- SPP — sourceA ChIP-seq peak calling algorithm, implemented as an R package, that accounts for the offset in forward-strand and reverse-strand reads to improve resolution, compares enrichment in signal to background or control experiments, and can also estimate whether the available number of reads is sufficient to achieve saturation, meaning that additional reads would not allow identification of additional peaks. SPP will be used in the ENCODE 3 uniform peak calling pipeline.Software type: peak caller